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If the previous version and the newly installed executable file are the same 64-bit version or 32-bit version, there should be no problem with overwriting the previous version.
Just in case, if you export HKEY_CURRENT_USER\Software\Thingamahoochie\WinMerge with regedit, you can restore the settings even if you uninstall if overwrite installation fails.

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Answer selected by TheRealSaiph
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